Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  • Interacting with Oscar
  • Installing XNAT2BIDS

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  1. XNAT to BIDS

Exporting to BIDS using Oscar

PreviousXNAT2BIDS SoftwareNextOscar Utility Script

Last updated 1 year ago

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Interacting with Oscar

You can connect to Oscar via different methods. You can , you can ), or if your editor can connect to remote servers, (VSCode is great!). If this is your first time using Oscar and you are new to unix command line, we recommend connecting via the Desktop GUI on Open OnDemand.

If you connect to Oscar via SSH or the OOD shell access app, you arrive at a login node, we will need to wrap our commands in a batch file or use an interactive session. You can learn more about running jobs in the Oscar . Please remember not to run processing on the login nodes

Installing XNAT2BIDS

🎉 Skip - You will not need to install any software. We keep a Singularity image of the most recent tagged release of in Oscar. If this is the first time that you hear the word Singularity image don't worry, we will expand more on that soon.

ssh using your terminal
connect via the Desktop GUI or OSCAR shell access apps on Open OnDemand(OOD
you can connect via your favorite IDE
docs
xnat-tools